function modelMetaData = modelCitations()
%generates metadata for the models indicated below
%
%OUTPUT
% modelMetaData         Cell array, where each row is metadata for one model
%                       with five columns: species, modelID, fileName, PMID, doi.

oriFolder = pwd;

%Testing modelCitations directory switch
find = what('testModels'); 
test_directory = find.path; 
cd(test_directory);

%Initial unsorted file
%Each row has the following columns: species, modelID, fileName, PMID, doi;
modelMetaData={...
'Homo sapiens','Recon1.0','09.17.09.Recon1','17267599','';...%version
'Homo sapiens','Recon2.05','Recon205_20150128','23455439','';...%version
'Homo sapiens','Recon2.04','Recon2_v04','23455439','';...%version
'Homo sapiens','HMR2.0','HMRdatabase2','26209309','';...%version
'Homo sapiens','Recon2.2','Recon22','27358602','';...%version
'Homo sapiens','Recon3D','2017_04_28_Recon3d','','';...%version
'Escherichia coli','core','Ecoli_core','','doi:10.1128/ecosalplus.10.2.1';...
'Lactococcus lactis subsp. MG1363','','L_lactis_MG1363','23974365','';...
'Streptococcus thermophilus','','Sc_thermophilis_rBioNet','19346354','';...%is this the Pastink et al one?
'Thermotoga maritima','v1','T_Maritima','19762644','';...
'Escherichia coli','iAF1260','iAF1260','17593909','';...
'Methanosarcina barkeri','iAF692','iAF692','16738551','';...
'Bacteroides thetaiotaomicron','iAH991','iAH991','23022739','';...%not in Palsson list
'Dehalococcoides ethenogenes','iAI549','iAI549','20811585','';...
'Yersinia pestis','iAN840m','iAN840m','19396373','';...% Yersinia pestis, S 825 x 1020,  Navid and Almaas, iAN818m?
'Bacillus subtilis','iBsu1103','iBsu1103','19555510','';...
'Clostridium beijerinckii','iCB925','iCB925','21846360','';...
'Helicobacter pylori','iIT341','iIT341','16077130','';...
'Synechocystis sp.','iJN678','iJN678','22308420','';...
'Pseudomonas putida','iJN746','iJN746','18793442','';...%not in Palsson list
'Escherichia coli','iJO1366','iJO1366','21988831','';...
'Pseudomonas putida','iJP815','iJP815','18974823','';...
'Escherichia coli','iJR904','iJR904','12952533','';...
'Burkholderia cenocepacia','iKF1028','iKF1028','21609491','';...%not in Palsson list
'Methanosarcina acetivorans','iMB745','iMB745','22139506','';...
'Saccharomyces cerevisiae','iMM904','iMM904','19321003','';...
'Saccharomyces cerevisiae','iND750','iND750','15197165','';...
'Mycobacterium tuberculosis','iNJ661','iNJ661','17555602','';...
'Rhodobacter sphaeroides','iRsp1095','iRsp1095','21777427','';...%not in Palsson list
'Staphylococcus aureus','iSB619','iSB619','15752426','';...'
'Mus musculus','iSS1393','iSS1393','23022739','';...%not in Palsson list
'Plasmodium falciparum','iTH366','iTH366','20823846','';...%not in Palsson list
'Thermotoga maritima','iTZ479v2','iTZ479_v2','','doi:10.1016/j.ijhydene.2012.06.032';...%not in Palsson list
'Klebsiella pneumoniae','iYL1228','iYL1228','21296962',''};

%Correct file output for comparison
%modelComparator = {'Bacillus subtilis','iBsu1103','iBsu1103','19555510','';'Bacteroides thetaiotaomicron','iAH991','iAH991','23022739','';'Burkholderia cenocepacia','iKF1028','iKF1028','21609491','';'Clostridium beijerinckii','iCB925','iCB925','21846360','';'Dehalococcoides ethenogenes','iAI549','iAI549','20811585','';'Escherichia coli','core','Ecoli_core','','doi:10.1128/ecosalplus.10.2.1';'Escherichia coli','iAF1260','iAF1260','17593909','';'Escherichia coli','iJO1366','iJO1366','21988831','';'Escherichia coli','iJR904','iJR904','12952533','';'Helicobacter pylori','iIT341','iIT341','16077130','';'Homo sapiens','Recon2.05','Recon205_20150128','23455439','';'Klebsiella pneumoniae','iYL1228','iYL1228','21296962','';'Lactococcus lactis subsp. MG1363','','L_lactis_MG1363','23974365','';'Methanosarcina acetivorans','iMB745','iMB745','22139506','';'Methanosarcina barkeri','iAF692','iAF692','16738551','';'Mus musculus','iSS1393','iSS1393','23022739','';'Mycobacterium tuberculosis','iNJ661','iNJ661','17555602','';'Plasmodium falciparum','iTH366','iTH366','20823846','';'Pseudomonas putida','iJN746','iJN746','18793442','';'Pseudomonas putida','iJP815','iJP815','18974823','';'Rhodobacter sphaeroides','iRsp1095','iRsp1095','21777427','';'Saccharomyces cerevisiae','iMM904','iMM904','19321003','';'Saccharomyces cerevisiae','iND750','iND750','15197165','';'Staphylococcus aureus','iSB619','iSB619','15752426','';'Streptococcus thermophilus','','Sc_thermophilis_rBioNet','19346354','';'Synechocystis sp.','iJN678','iJN678','22308420','';'Thermotoga maritima','v1','T_Maritima','19762644','';'Thermotoga maritima','iTZ479v2','iTZ479_v2','','doi:10.1016/j.ijhydene.2012.06.032';'Yersinia pestis','iAN840m','iAN840m','19396373',''};

%sort the models alphabetically by the species
[tmp,indicies]=sort(modelMetaData(:,1));
modelMetaData=modelMetaData(indicies,:);

%Test check parameters based upon the data array
%if ~isequal(modelComparator, modelMetaData)
%    fprintf('\nIncorrect model parameters for modelCitations\n');
%    x=0;
%else 
%    fprintf('\nTest for modelCitations suceeded\n')
%end
cd(oriFolder);
end

%old code
% function modelMetaData=modelCitations()
% %generates metadata for the models indicated below
% %
% %OUTPUT
% % modelMetaData         Cell array, where each row is metadata for one model
% %                       with five columns: species, version, fileName, PMID, doi.
% 
% %Each row: species, version, fileName, PMID, doi;
% modelMetaData={...
% 'Escherichia coli','core','Ecoli_core','','doi:10.1128/ecosalplus.10.2.1';...
% 'Lactococcus lactis subsp. MG1363','','L_lactis_MG1363','23974365','';...
% 'Homo sapiens','Recon2.05','Recon205_20150128','23455439','';...%version
% 'Homo sapiens','Recon2.04','121114_Recon2betaModel','23455439','';...%version
% 'Streptococcus thermophilus','','Sc_thermophilis_rBioNet','19346354','';...%is this the Pastink et al one?
% 'Thermotoga maritima','v1','T_Maritima','19762644','';...
% 'Escherichia coli','iAF1260','iAF1260','17593909','';...
% 'Methanosarcina barkeri','iAF692','iAF692','16738551','';...
% 'Bacteroides thetaiotaomicron','iAH991','iAH991','23022739','';...%not in Palsson list
% 'Dehalococcoides ethenogenes','iAI549','iAI549','20811585','';...
% 'Yersinia pestis','iAN840m','iAN840m','19396373','';...% Yersinia pestis, S 825 x 1020,  Navid and Almaas, iAN818m?
% 'Bacillus subtilis','iBsu1103','iBsu1103','19555510','';...
% 'Clostridium beijerinckii','iCB925','iCB925','21846360','';...
% 'Helicobacter pylori','iIT341','iIT341','16077130','';...
% 'Synechocystis sp.','iJN678','iJN678','22308420','';...
% 'Pseudomonas putida','iJN746','iJN746','18793442','';...%not in Palsson list
% 'Escherichia coli','iJO1366','iJO1366','21988831','';...
% 'Pseudomonas putida','iJP815','iJP815','18974823','';...
% 'Escherichia coli','iJR904','iJR904','12952533','';...
% 'Burkholderia cenocepacia','iKF1028','iKF1028','21609491','';...%not in Palsson list
% 'Methanosarcina acetivorans','iMB745','iMB745','22139506','';...
% 'Saccharomyces cerevisiae','iMM904','iMM904','19321003','';...
% 'Saccharomyces cerevisiae','iND750','iND750','15197165','';...
% 'Mycobacterium tuberculosis','iNJ661','iNJ661','17555602','';...
% 'Rhodobacter sphaeroides','iRsp1095','iRsp1095','21777427','';...%not in Palsson list
% 'Staphylococcus aureus','iSB619','iSB619','15752426','';...'
% 'Mus musculus','iSS1393','iSS1393','23022739','';...%not in Palsson list
% 'Plasmodium falciparum','iTH366','iTH366','20823846','';...%not in Palsson list
% 'Thermotoga maritima','iTZ479v2','iTZ479_v2','','doi:10.1016/j.ijhydene.2012.06.032';...%not in Palsson list
% 'Klebsiella pneumoniae','iYL1228','iYL1228','21296962',''};
% 
% %sort the models alphabetically by the species
% [tmp,indicies]=sort(modelMetaData(:,1));
% modelMetaData=modelMetaData(indicies,:);
